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This Month in Bioinformatics: Research Updates of September 2020

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Bioinformatics Monthly updates- September 2020

Some of the important findings made this month in bioinformatics are mentioned in this article.

1. A novel universal primer pair for prokaryotes

A novel primer (Pro341FB) has been designed Planctomycetes phylum [1]. This primer is designed by making a minor modification in the previously known primer called Pro341F. This newly designed primer is more sensitive than the Pro341F primer. It has been validated by a 16 NGS survey on microbial communities from various wastewater treatment plants. It was found that this primer is capable of performing 5 folds in revealing more members of prokaryotes. For further information, read here.

2. New Tool for Ion Torrent Sequence Files Compression

The new software has been developed for efficient compression of Ion Torrent sequence files such as BAM files into CRAM files. This software is known as IonCRAM [2]. IonCRAM is a lossless reference-based compression tool. It is capable of compressing BAM files into archiving CRAM files such that it could save up to 43% of space. This is open-source software and is freely available at GitHub, CodeOcean, and http://ioncram.saudigenomeproject.com. For more information, read here and here.

3. New Program for Metagenomic Sequencing Data Analysis

MAIRA is a new software for taxonomic and functional analysis of long reads without requiring any external resource [3]. It can easily facilitate the execution of metagenomic analysis pipelines on a local computer. It is fast and allows users to perform several analyses in real-time including genus-level analysis and frame-shift alignment of DNA reads. The main advantage of this software is that it can be easily run on a laptop without any external source support, especially when we have to use workstations for large datasets. For further information, read here and here.

4. New database for Alzheimer’s disease

A new online database called AlzRiskMR has been developed for the impact of exposure factors on Alzheimer’s disease [4]. It is created by comprehensive analyses by two-sample Mendelian randomization (2SMR). AlzRiskMR is freely accessible on Github at the given URL: https://github.com/SDBMC/RiskFactors2AD. This database currently consists of 1870 sets of data of Genome-Wide Association Studies from the MR-Base and NHGRI-EBI GWAS Catalog database. For further information, read here.

5. New method for drug-drug interaction prediction

A novel method has been introduced to predict drug-drug interactions based on deep neural networks [5]. It predicts drug-drug interactions by extracting the network structure features of drugs from the drug-drug interaction network. The results have revealed that this method performs much better than the other methods of drug-drug interaction prediction. For further information, read here.

6. Drug-target interaction prediction using multi-label learning

DTI-MLCD is a community detection method based on multi-label classification for the prediction of drug-target interactions [6]. Chu et al., [6] has added 15,000 more positive drug-target interaction samples to the gold standard data set. The results show that DTI-MLCD outperforms other machine learning and other existing methods used for drug-target interaction prediction. For further information, read here.

References

  1. Mazzoli, L., Munz, G., Lotti, T., & Ramazzotti, M. (2020). A novel universal primer pair for prokaryotes with improved performances for anammox containing communities. Scientific Reports10(1), 1-7.
  2. Shokrof, M., Abouelhoda, M. IonCRAM: a reference-based compression tool for ion torrent sequence files. BMC Bioinformatics 21, 397 (2020).
  3. Albrecht, B., Bağcı, C., & Huson, D. H. (2020). MAIRA-real-time taxonomic and functional analysis of long reads on a laptop. BMC bioinformatics21(13), 1-12.
  4. Wang, Z., Meng, L., Liu, H., Shen, L., & Ji, H. F. (2020). AlzRiskMR database: an online database for the impact of exposure factors on Alzheimer’s disease. Briefings in Bioinformatics.
  5. Feng, Y. H., Zhang, S. W., & Shi, J. Y. (2020). DPDDI: a deep predictor for drug-drug interactions. BMC bioinformatics21(1), 1-15.
  6. Chu, Y., Shan, X., Chen, T., Jiang, M., Wang, Y., Wang, Q., … & Wei, D. Q. (2020). DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method. Briefings in Bioinformatics.

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VS_Analysis: A Python package to perform post-virtual screening analysis

Dr. Muniba Faiza

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VS_Analysis: A Python package to perform post-virtual screening analysis

Virtual screening (VS) is a crucial aspect of bioinformatics. As you may already know, there are various tools available for this purpose, including both paid and freely accessible options such as Autodock Vina. Conducting virtual screening with Autodock Vina requires less effort than analyzing its results. However, the analysis process can be challenging due to the large number of output files generated. To address this, we offer a comprehensive Python package designed to automate the analysis of virtual screening results.

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Proteins shape analyses reveal novel forms and connections.

Dr. Muniba Faiza

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Protein shape analyses reveal novel forms and connections.

A new study has revealed new forms of proteins that have never been seen before along with unexpected connections. Last year, Google DeepMind predicted the structure of all known proteins from organisms using AlphaFold [1].

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What is MANE project?

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What is mane project?

MANE is a collaborative project between NCBI and EMBL-EBI. It stands for Matched Annotation from NCBI and EMBL-EBI [1]. The datasets provided by NCBI and EMBL-EBI on the human genome are not identical across every gene.

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This Month in Bioinformatics- Research Updates of March 2022

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This Month in Bioinformatics- Research Updates of March 2022

Here are the latest research developments in the field of bioinformatics made in the month of March 2022. (more…)

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This month in Bioinformatics- Research Updates of November 2021

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This month in Bioinformatics- Research Updates of November 2021

We summarize the latest research published this month in the field of bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of October 2021

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In this article, we summarize the latest interesting findings made this month in bioinformatics. (more…)

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BLAST+ 2.12.0- A more efficient version of BLAST is available

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BLAST+ 2.12.0- New version

A new more efficient version of BLAST+ 2.12.o is available now [1]. This version provides more efficient multithreaded searches. (more…)

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This Month in Bioinformatics- Research Updates of June 2021

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This Month in Bioinformatics- Research Updates of June 2021

In this article, we summarize the latest interesting findings made this month of June in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of May 2021

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This Month in Bioinformatics- Research Updates of May 2021

In this article, we summarize the latest interesting findings made this month in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of April 2021

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This Month in Bioinformatics- Research Updates of April 2021

In this article, we summarize the latest interesting findings made this month in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of March 2021

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Bioinformatics Monthly Research Updates- March 2021

Here, we summarize the latest interesting findings made this month in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of February 2021

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Monthly Research Updates- February 2021

We summarize the research done in bioinformatics in the month of February. (more…)

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This Month in Bioinformatics- Research Updates of January 2021

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This month in Bioinformatics- January 2021

In this article, we summarize the main findings made in bioinformatics this month. (more…)

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This Month in Bioinformatics- Research Updates of December 2020

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This Month in Bioinformatics- Research Updates of December 2020

In this article, we summarize the latest research in bioinformatics published this month. (more…)

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Join Bioinformatics Review Research Group

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We are going to lead a few bioinformatics research projects. For that, we are creating a new research group of Bioinformatics Review. (more…)

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This Month in Bioinformatics- Research Updates of November 2020

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Research updates of bioinformatics- November 2020

In this article, we summarize the latest research in bioinformatics published this month. (more…)

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This Month in Bioinformatics- Research Updates of October 2020

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monthly-october updates bioinformatics

Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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This Month in Bioinformatics: Research Updates of August 2020

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Bioinformatics Research Updates- August 2020

Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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This month in Bioinformatics: Research Updates of July 2020

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This month in Bioinformatics

Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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Inviting Nominations for ‘Top 5 Bioinformaticians in India 2020’

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Bioinformaticians Awards

Bioinformatics Review compiles a list of top bioinformaticians every two years. We are inviting nominations for the second edition of this award after the 2018 List. We invite you to contribute to this endeavor by nominating your colleague or friends if you think they can make it to our list.

Nominations start from 20th June 2020 till 15th August 2020. All the nominees will be informed via email on 5th September 2020. We use a well-established ranking method called ScipRank. Our data collection is open-source. ScipRank methodology is publicly available for scrutiny.

Also, we are completing 5th year of success in Bioinformatics Review this year. On this occasion, we are organizing an International Conference on Advanced Research in Bioinformatics 2020. The award will be declared at the conclusion of ConARB 2020 –  3 & 4th Oct 2020).

We invite you to contribute to this endeavor by nominating your colleague or friends. You can also submit your papers, which if accepted, can be presented at the conference.

We have set up a dedicated portal for ConARB 2020 accessible here https://conarb.bioinformaticsreview.com.
To attend or to submit your abstract or to nominate someone, kindly visit this website. Accepted papers will be published in a special issue of Bioinformatics Review.

We are looking forward to your continued support, contributions, nominations, and suggestions for the conference as well as your active participation.

 

 

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